In cancer research, it is becoming increasingly critical to study tumor cells in the context of their microenvironment (e.g. in the presence of stromal and/or immune cells and within a relevant 3D niche). This is not only important for understanding fundamental tumor biology, but also to develop the next generation of anti-tumor therapeutics and interventions. The ability to study tumor cell interactions with other niche components (fibroblasts, MDSCs, macrophages and dendritic cells (DCs), regulatory and effector T cells, B cells, tumor-ECM, tumor vasculature etc.) in a quantitative manner, within highly-controlled synthetic microenvironments, could provide significant new information on the growth, proliferation, cell-cell and cell-matrix communication of various tumors while allowing study of how external manipulations (e.g. drugs, immunotherapies, radiation therapy etc.) affect tumors in a more native-like microenvironment.
In vitro 3D systems of synthetic or ECM-derived biomaterials containing cells or organoids have become essential for better understanding of cell biology, unraveling complex disease processes, and developing new biomedical materials to restore function in diseased tissues or deliver therapeutic cells. Biological assays inherently suffer from high “noise” that limits experimental reproducibility. Cells in particular are highly sensitive to manipulations and changes to their microenvironment. Thus, measurement-confidence in cell-behavior requires high replicate numbers to generate high statistical power, reduce false positives, and identify subtle changes. Unfortunately, existing methods are time-intensive, low-throughput, destructive, or limit further sample manipulation. However, such approaches suffer from a lack of high throughput analytical methods that allows rapid measurement of many cell parameters inside 3D niches in a non-destructive manner with high statistical confidence.
Flow cytometry allows for the collection of a large number of unique events in a short time period, which can be combined to build a picture, characteristic of a large population. Because multiple fluorescent channels can be used concurrently, flow cytometry enables the user to precisely define multiple values of interest and use these to gate for specific sections of interest. However, fluorescence alone gives very little multiplexing capability compared to hundreds of parameters that one can envision studying. Even the CyTOF method allows ˜40-60 variables to be studied, but uses a destructive mass spec-based process.
It is with respect to these and other considerations that the various aspects of the disclosed technology as described below are presented.